Starting phenix.real_space_refine on Mon Aug 25 16:21:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u66_41946/08_2025/8u66_41946.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u66_41946/08_2025/8u66_41946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u66_41946/08_2025/8u66_41946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u66_41946/08_2025/8u66_41946.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u66_41946/08_2025/8u66_41946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u66_41946/08_2025/8u66_41946.map" } resolution = 2.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 128 5.16 5 C 17968 2.51 5 N 5064 2.21 5 O 6181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29365 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "B" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 125 Classifications: {'water': 125} Link IDs: {None: 124} Chain: "C" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Classifications: {'water': 121} Link IDs: {None: 120} Chain: "E" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 125 Classifications: {'water': 125} Link IDs: {None: 124} Chain: "F" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Classifications: {'water': 121} Link IDs: {None: 120} Chain: "G" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Classifications: {'water': 121} Link IDs: {None: 120} Chain: "H" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Time building chain proxies: 7.10, per 1000 atoms: 0.24 Number of scatterers: 29365 At special positions: 0 Unit cell: (122.85, 122.85, 108.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 128 16.00 P 16 15.00 Mg 8 11.99 O 6181 8.00 N 5064 7.00 C 17968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6464 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 24 sheets defined 54.2% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 Processing helix chain 'A' and resid 42 through 56 Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 98 through 107 Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.614A pdb=" N PHE A 113 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 140 through 149 Processing helix chain 'A' and resid 167 through 182 Processing helix chain 'A' and resid 199 through 219 Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 255 through 259 Processing helix chain 'A' and resid 259 through 274 Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.553A pdb=" N ARG A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL A 300 " --> pdb=" O HIS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 337 Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 398 through 419 Processing helix chain 'A' and resid 422 through 436 removed outlier: 5.851A pdb=" N ARG A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 448 Processing helix chain 'B' and resid 13 through 18 Processing helix chain 'B' and resid 42 through 56 Processing helix chain 'B' and resid 62 through 68 Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 90 through 94 Processing helix chain 'B' and resid 98 through 107 Processing helix chain 'B' and resid 109 through 113 removed outlier: 3.614A pdb=" N PHE B 113 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 140 through 149 Processing helix chain 'B' and resid 167 through 182 Processing helix chain 'B' and resid 199 through 219 Processing helix chain 'B' and resid 232 through 246 Processing helix chain 'B' and resid 255 through 259 Processing helix chain 'B' and resid 259 through 274 Processing helix chain 'B' and resid 284 through 289 removed outlier: 3.552A pdb=" N ARG B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL B 300 " --> pdb=" O HIS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 337 Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 389 through 394 Processing helix chain 'B' and resid 398 through 419 Processing helix chain 'B' and resid 422 through 436 removed outlier: 5.851A pdb=" N ARG B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 Processing helix chain 'C' and resid 13 through 18 Processing helix chain 'C' and resid 42 through 56 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 69 through 74 Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 98 through 107 Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.614A pdb=" N PHE C 113 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 132 Processing helix chain 'C' and resid 140 through 149 Processing helix chain 'C' and resid 167 through 182 Processing helix chain 'C' and resid 199 through 219 Processing helix chain 'C' and resid 232 through 246 Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 259 through 274 Processing helix chain 'C' and resid 284 through 289 removed outlier: 3.553A pdb=" N ARG C 289 " --> pdb=" O ALA C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL C 300 " --> pdb=" O HIS C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 337 Processing helix chain 'C' and resid 369 through 371 No H-bonds generated for 'chain 'C' and resid 369 through 371' Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 398 through 419 Processing helix chain 'C' and resid 422 through 436 removed outlier: 5.850A pdb=" N ARG C 428 " --> pdb=" O LEU C 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 448 Processing helix chain 'D' and resid 13 through 18 Processing helix chain 'D' and resid 42 through 56 Processing helix chain 'D' and resid 62 through 68 Processing helix chain 'D' and resid 69 through 74 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 98 through 107 Processing helix chain 'D' and resid 109 through 113 removed outlier: 3.614A pdb=" N PHE D 113 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 140 through 149 Processing helix chain 'D' and resid 167 through 182 Processing helix chain 'D' and resid 199 through 219 Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 259 through 274 Processing helix chain 'D' and resid 284 through 289 removed outlier: 3.553A pdb=" N ARG D 289 " --> pdb=" O ALA D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL D 300 " --> pdb=" O HIS D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 337 Processing helix chain 'D' and resid 369 through 371 No H-bonds generated for 'chain 'D' and resid 369 through 371' Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 389 through 394 Processing helix chain 'D' and resid 398 through 419 Processing helix chain 'D' and resid 422 through 436 removed outlier: 5.851A pdb=" N ARG D 428 " --> pdb=" O LEU D 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN D 429 " --> pdb=" O ALA D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 448 Processing helix chain 'E' and resid 13 through 18 Processing helix chain 'E' and resid 42 through 56 Processing helix chain 'E' and resid 62 through 68 Processing helix chain 'E' and resid 69 through 74 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 98 through 107 Processing helix chain 'E' and resid 109 through 113 removed outlier: 3.613A pdb=" N PHE E 113 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 132 Processing helix chain 'E' and resid 140 through 149 Processing helix chain 'E' and resid 167 through 182 Processing helix chain 'E' and resid 199 through 219 Processing helix chain 'E' and resid 232 through 246 Processing helix chain 'E' and resid 255 through 259 Processing helix chain 'E' and resid 259 through 274 Processing helix chain 'E' and resid 284 through 289 removed outlier: 3.553A pdb=" N ARG E 289 " --> pdb=" O ALA E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL E 300 " --> pdb=" O HIS E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 337 Processing helix chain 'E' and resid 369 through 371 No H-bonds generated for 'chain 'E' and resid 369 through 371' Processing helix chain 'E' and resid 372 through 381 Processing helix chain 'E' and resid 389 through 394 Processing helix chain 'E' and resid 398 through 419 Processing helix chain 'E' and resid 422 through 436 removed outlier: 5.850A pdb=" N ARG E 428 " --> pdb=" O LEU E 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN E 429 " --> pdb=" O ALA E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 448 Processing helix chain 'F' and resid 13 through 18 Processing helix chain 'F' and resid 42 through 56 Processing helix chain 'F' and resid 62 through 68 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 98 through 107 Processing helix chain 'F' and resid 109 through 113 removed outlier: 3.614A pdb=" N PHE F 113 " --> pdb=" O VAL F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 132 Processing helix chain 'F' and resid 140 through 149 Processing helix chain 'F' and resid 167 through 182 Processing helix chain 'F' and resid 199 through 219 Processing helix chain 'F' and resid 232 through 246 Processing helix chain 'F' and resid 255 through 259 Processing helix chain 'F' and resid 259 through 274 Processing helix chain 'F' and resid 284 through 289 removed outlier: 3.553A pdb=" N ARG F 289 " --> pdb=" O ALA F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL F 300 " --> pdb=" O HIS F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 337 Processing helix chain 'F' and resid 369 through 371 No H-bonds generated for 'chain 'F' and resid 369 through 371' Processing helix chain 'F' and resid 372 through 381 Processing helix chain 'F' and resid 389 through 394 Processing helix chain 'F' and resid 398 through 419 Processing helix chain 'F' and resid 422 through 436 removed outlier: 5.850A pdb=" N ARG F 428 " --> pdb=" O LEU F 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN F 429 " --> pdb=" O ALA F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 448 Processing helix chain 'G' and resid 13 through 18 Processing helix chain 'G' and resid 42 through 56 Processing helix chain 'G' and resid 62 through 68 Processing helix chain 'G' and resid 69 through 74 Processing helix chain 'G' and resid 90 through 94 Processing helix chain 'G' and resid 98 through 107 Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.614A pdb=" N PHE G 113 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 132 Processing helix chain 'G' and resid 140 through 149 Processing helix chain 'G' and resid 167 through 182 Processing helix chain 'G' and resid 199 through 219 Processing helix chain 'G' and resid 232 through 246 Processing helix chain 'G' and resid 255 through 259 Processing helix chain 'G' and resid 259 through 274 Processing helix chain 'G' and resid 284 through 289 removed outlier: 3.553A pdb=" N ARG G 289 " --> pdb=" O ALA G 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL G 300 " --> pdb=" O HIS G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 337 Processing helix chain 'G' and resid 369 through 371 No H-bonds generated for 'chain 'G' and resid 369 through 371' Processing helix chain 'G' and resid 372 through 381 Processing helix chain 'G' and resid 389 through 394 Processing helix chain 'G' and resid 398 through 419 Processing helix chain 'G' and resid 422 through 436 removed outlier: 5.850A pdb=" N ARG G 428 " --> pdb=" O LEU G 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN G 429 " --> pdb=" O ALA G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 448 Processing helix chain 'H' and resid 13 through 18 Processing helix chain 'H' and resid 42 through 56 Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 69 through 74 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 98 through 107 Processing helix chain 'H' and resid 109 through 113 removed outlier: 3.614A pdb=" N PHE H 113 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 140 through 149 Processing helix chain 'H' and resid 167 through 182 Processing helix chain 'H' and resid 199 through 219 Processing helix chain 'H' and resid 232 through 246 Processing helix chain 'H' and resid 255 through 259 Processing helix chain 'H' and resid 259 through 274 Processing helix chain 'H' and resid 284 through 289 removed outlier: 3.553A pdb=" N ARG H 289 " --> pdb=" O ALA H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL H 300 " --> pdb=" O HIS H 296 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 337 Processing helix chain 'H' and resid 369 through 371 No H-bonds generated for 'chain 'H' and resid 369 through 371' Processing helix chain 'H' and resid 372 through 381 Processing helix chain 'H' and resid 389 through 394 Processing helix chain 'H' and resid 398 through 419 Processing helix chain 'H' and resid 422 through 436 removed outlier: 5.850A pdb=" N ARG H 428 " --> pdb=" O LEU H 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN H 429 " --> pdb=" O ALA H 425 " (cutoff:3.500A) Processing helix chain 'H' and resid 438 through 448 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 81 removed outlier: 6.732A pdb=" N TYR A 86 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE A 80 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP A 123 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG A 34 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU A 121 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU A 36 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU A 119 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 157 removed outlier: 6.394A pdb=" N LEU A 155 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS A 313 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 251 " --> pdb=" O HIS A 278 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N HIS A 280 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL A 253 " --> pdb=" O HIS A 280 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS A 224 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N MET A 252 " --> pdb=" O HIS A 224 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU A 226 " --> pdb=" O MET A 252 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ASP A 254 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N THR A 186 " --> pdb=" O TRP A 225 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ASN A 227 " --> pdb=" O THR A 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 81 removed outlier: 6.732A pdb=" N TYR B 86 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE B 80 " --> pdb=" O THR B 84 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP B 123 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG B 34 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU B 121 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU B 36 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU B 119 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 155 through 157 removed outlier: 6.394A pdb=" N LEU B 155 " --> pdb=" O PHE B 386 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS B 313 " --> pdb=" O CYS B 279 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B 251 " --> pdb=" O HIS B 278 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS B 280 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 253 " --> pdb=" O HIS B 280 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N HIS B 224 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N MET B 252 " --> pdb=" O HIS B 224 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU B 226 " --> pdb=" O MET B 252 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ASP B 254 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR B 186 " --> pdb=" O TRP B 225 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ASN B 227 " --> pdb=" O THR B 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AA7, first strand: chain 'C' and resid 76 through 81 removed outlier: 6.732A pdb=" N TYR C 86 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE C 80 " --> pdb=" O THR C 84 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP C 123 " --> pdb=" O ALA C 32 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG C 34 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU C 121 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU C 36 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU C 119 " --> pdb=" O GLU C 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 155 through 157 removed outlier: 6.395A pdb=" N LEU C 155 " --> pdb=" O PHE C 386 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS C 313 " --> pdb=" O CYS C 279 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE C 251 " --> pdb=" O HIS C 278 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS C 280 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL C 253 " --> pdb=" O HIS C 280 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N HIS C 224 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET C 252 " --> pdb=" O HIS C 224 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU C 226 " --> pdb=" O MET C 252 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ASP C 254 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR C 186 " --> pdb=" O TRP C 225 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ASN C 227 " --> pdb=" O THR C 186 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AB1, first strand: chain 'D' and resid 76 through 81 removed outlier: 6.732A pdb=" N TYR D 86 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE D 80 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP D 123 " --> pdb=" O ALA D 32 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG D 34 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU D 121 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N GLU D 36 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU D 119 " --> pdb=" O GLU D 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 155 through 157 removed outlier: 6.394A pdb=" N LEU D 155 " --> pdb=" O PHE D 386 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS D 313 " --> pdb=" O CYS D 279 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE D 251 " --> pdb=" O HIS D 278 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N HIS D 280 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL D 253 " --> pdb=" O HIS D 280 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS D 224 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET D 252 " --> pdb=" O HIS D 224 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU D 226 " --> pdb=" O MET D 252 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ASP D 254 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N THR D 186 " --> pdb=" O TRP D 225 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ASN D 227 " --> pdb=" O THR D 186 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 339 through 340 Processing sheet with id=AB4, first strand: chain 'E' and resid 76 through 81 removed outlier: 6.732A pdb=" N TYR E 86 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE E 80 " --> pdb=" O THR E 84 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP E 123 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG E 34 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU E 121 " --> pdb=" O ARG E 34 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU E 36 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU E 119 " --> pdb=" O GLU E 36 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 155 through 157 removed outlier: 6.394A pdb=" N LEU E 155 " --> pdb=" O PHE E 386 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS E 313 " --> pdb=" O CYS E 279 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE E 251 " --> pdb=" O HIS E 278 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS E 280 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL E 253 " --> pdb=" O HIS E 280 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS E 224 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET E 252 " --> pdb=" O HIS E 224 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU E 226 " --> pdb=" O MET E 252 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ASP E 254 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR E 186 " --> pdb=" O TRP E 225 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ASN E 227 " --> pdb=" O THR E 186 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 339 through 340 Processing sheet with id=AB7, first strand: chain 'F' and resid 76 through 81 removed outlier: 6.732A pdb=" N TYR F 86 " --> pdb=" O TYR F 78 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE F 80 " --> pdb=" O THR F 84 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP F 123 " --> pdb=" O ALA F 32 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG F 34 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU F 121 " --> pdb=" O ARG F 34 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU F 36 " --> pdb=" O LEU F 119 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU F 119 " --> pdb=" O GLU F 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 155 through 157 removed outlier: 6.395A pdb=" N LEU F 155 " --> pdb=" O PHE F 386 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS F 313 " --> pdb=" O CYS F 279 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE F 251 " --> pdb=" O HIS F 278 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS F 280 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL F 253 " --> pdb=" O HIS F 280 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N HIS F 224 " --> pdb=" O TYR F 250 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET F 252 " --> pdb=" O HIS F 224 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU F 226 " --> pdb=" O MET F 252 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ASP F 254 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR F 186 " --> pdb=" O TRP F 225 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ASN F 227 " --> pdb=" O THR F 186 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 339 through 340 Processing sheet with id=AC1, first strand: chain 'G' and resid 76 through 81 removed outlier: 6.732A pdb=" N TYR G 86 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE G 80 " --> pdb=" O THR G 84 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP G 123 " --> pdb=" O ALA G 32 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG G 34 " --> pdb=" O LEU G 121 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU G 121 " --> pdb=" O ARG G 34 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU G 36 " --> pdb=" O LEU G 119 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU G 119 " --> pdb=" O GLU G 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 155 through 157 removed outlier: 6.394A pdb=" N LEU G 155 " --> pdb=" O PHE G 386 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS G 313 " --> pdb=" O CYS G 279 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE G 251 " --> pdb=" O HIS G 278 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS G 280 " --> pdb=" O ILE G 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL G 253 " --> pdb=" O HIS G 280 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS G 224 " --> pdb=" O TYR G 250 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET G 252 " --> pdb=" O HIS G 224 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU G 226 " --> pdb=" O MET G 252 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ASP G 254 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR G 186 " --> pdb=" O TRP G 225 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ASN G 227 " --> pdb=" O THR G 186 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 339 through 340 Processing sheet with id=AC4, first strand: chain 'H' and resid 76 through 81 removed outlier: 6.731A pdb=" N TYR H 86 " --> pdb=" O TYR H 78 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE H 80 " --> pdb=" O THR H 84 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR H 84 " --> pdb=" O ILE H 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP H 123 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG H 34 " --> pdb=" O LEU H 121 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU H 121 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU H 36 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU H 119 " --> pdb=" O GLU H 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 155 through 157 removed outlier: 6.394A pdb=" N LEU H 155 " --> pdb=" O PHE H 386 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS H 313 " --> pdb=" O CYS H 279 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE H 251 " --> pdb=" O HIS H 278 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS H 280 " --> pdb=" O ILE H 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL H 253 " --> pdb=" O HIS H 280 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS H 224 " --> pdb=" O TYR H 250 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N MET H 252 " --> pdb=" O HIS H 224 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU H 226 " --> pdb=" O MET H 252 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ASP H 254 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR H 186 " --> pdb=" O TRP H 225 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ASN H 227 " --> pdb=" O THR H 186 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 339 through 340 1384 hydrogen bonds defined for protein. 3840 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.08 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4693 1.32 - 1.44: 8100 1.44 - 1.56: 16079 1.56 - 1.68: 16 1.68 - 1.81: 208 Bond restraints: 29096 Sorted by residual: bond pdb=" NZ KCX E 187 " pdb=" CX KCX E 187 " ideal model delta sigma weight residual 1.411 1.329 0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" NZ KCX F 187 " pdb=" CX KCX F 187 " ideal model delta sigma weight residual 1.411 1.331 0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" NZ KCX D 187 " pdb=" CX KCX D 187 " ideal model delta sigma weight residual 1.411 1.332 0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" NZ KCX H 187 " pdb=" CX KCX H 187 " ideal model delta sigma weight residual 1.411 1.334 0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" NZ KCX C 187 " pdb=" CX KCX C 187 " ideal model delta sigma weight residual 1.411 1.334 0.077 2.00e-02 2.50e+03 1.47e+01 ... (remaining 29091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 39172 2.64 - 5.28: 267 5.28 - 7.92: 13 7.92 - 10.56: 12 10.56 - 13.20: 8 Bond angle restraints: 39472 Sorted by residual: angle pdb=" C3 CAP H 502 " pdb=" C4 CAP H 502 " pdb=" C5 CAP H 502 " ideal model delta sigma weight residual 111.00 124.20 -13.20 3.00e+00 1.11e-01 1.94e+01 angle pdb=" C3 CAP E 502 " pdb=" C4 CAP E 502 " pdb=" C5 CAP E 502 " ideal model delta sigma weight residual 111.00 124.18 -13.18 3.00e+00 1.11e-01 1.93e+01 angle pdb=" C3 CAP G 502 " pdb=" C4 CAP G 502 " pdb=" C5 CAP G 502 " ideal model delta sigma weight residual 111.00 124.18 -13.18 3.00e+00 1.11e-01 1.93e+01 angle pdb=" C3 CAP D 502 " pdb=" C4 CAP D 502 " pdb=" C5 CAP D 502 " ideal model delta sigma weight residual 111.00 124.18 -13.18 3.00e+00 1.11e-01 1.93e+01 angle pdb=" C3 CAP B 502 " pdb=" C4 CAP B 502 " pdb=" C5 CAP B 502 " ideal model delta sigma weight residual 111.00 124.16 -13.16 3.00e+00 1.11e-01 1.92e+01 ... (remaining 39467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.78: 16529 34.78 - 69.56: 507 69.56 - 104.34: 84 104.34 - 139.12: 4 139.12 - 173.90: 4 Dihedral angle restraints: 17128 sinusoidal: 6952 harmonic: 10176 Sorted by residual: dihedral pdb=" C3 CAP H 502 " pdb=" C CAP H 502 " pdb=" C2 CAP H 502 " pdb=" O6 CAP H 502 " ideal model delta sinusoidal sigma weight residual 81.86 -92.04 173.90 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C3 CAP D 502 " pdb=" C CAP D 502 " pdb=" C2 CAP D 502 " pdb=" O6 CAP D 502 " ideal model delta sinusoidal sigma weight residual 81.86 -92.04 173.90 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C3 CAP E 502 " pdb=" C CAP E 502 " pdb=" C2 CAP E 502 " pdb=" O6 CAP E 502 " ideal model delta sinusoidal sigma weight residual 81.86 -92.03 173.89 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 17125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.350: 4144 0.350 - 0.700: 0 0.700 - 1.050: 0 1.050 - 1.400: 0 1.400 - 1.750: 8 Chirality restraints: 4152 Sorted by residual: chirality pdb=" C4 CAP B 502 " pdb=" C3 CAP B 502 " pdb=" C5 CAP B 502 " pdb=" O4 CAP B 502 " both_signs ideal model delta sigma weight residual False -2.47 -0.72 -1.75 2.00e-01 2.50e+01 7.66e+01 chirality pdb=" C4 CAP H 502 " pdb=" C3 CAP H 502 " pdb=" C5 CAP H 502 " pdb=" O4 CAP H 502 " both_signs ideal model delta sigma weight residual False -2.47 -0.72 -1.75 2.00e-01 2.50e+01 7.63e+01 chirality pdb=" C4 CAP G 502 " pdb=" C3 CAP G 502 " pdb=" C5 CAP G 502 " pdb=" O4 CAP G 502 " both_signs ideal model delta sigma weight residual False -2.47 -0.72 -1.75 2.00e-01 2.50e+01 7.63e+01 ... (remaining 4149 not shown) Planarity restraints: 5168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA KCX F 187 " -0.009 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" C KCX F 187 " 0.033 2.00e-02 2.50e+03 pdb=" O KCX F 187 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP F 188 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA KCX A 187 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C KCX A 187 " 0.033 2.00e-02 2.50e+03 pdb=" O KCX A 187 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP A 188 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA KCX B 187 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C KCX B 187 " -0.033 2.00e-02 2.50e+03 pdb=" O KCX B 187 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP B 188 " 0.011 2.00e-02 2.50e+03 ... (remaining 5165 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 188 2.48 - 3.08: 21060 3.08 - 3.69: 51577 3.69 - 4.29: 83912 4.29 - 4.90: 129116 Nonbonded interactions: 285853 Sorted by model distance: nonbonded pdb=" OD1 ASP E 189 " pdb="MG MG E 501 " model vdw 1.869 2.170 nonbonded pdb=" OD1 ASP G 189 " pdb="MG MG G 501 " model vdw 1.870 2.170 nonbonded pdb=" OD1 ASP C 189 " pdb="MG MG C 501 " model vdw 1.871 2.170 nonbonded pdb=" OD1 ASP H 189 " pdb="MG MG H 501 " model vdw 1.871 2.170 nonbonded pdb=" OD1 ASP B 189 " pdb="MG MG B 501 " model vdw 1.872 2.170 ... (remaining 285848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 29.700 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 29096 Z= 0.159 Angle : 0.561 13.198 39472 Z= 0.263 Chirality : 0.085 1.750 4152 Planarity : 0.003 0.022 5168 Dihedral : 16.747 173.903 10664 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.28 % Allowed : 11.41 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.15), residues: 3544 helix: 1.76 (0.13), residues: 1664 sheet: 0.50 (0.25), residues: 424 loop : 1.32 (0.18), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 249 TYR 0.016 0.001 TYR C 263 PHE 0.012 0.001 PHE E 297 TRP 0.009 0.001 TRP G 354 HIS 0.003 0.001 HIS E 311 Details of bonding type rmsd covalent geometry : bond 0.00351 (29096) covalent geometry : angle 0.56069 (39472) hydrogen bonds : bond 0.14111 ( 1384) hydrogen bonds : angle 6.81192 ( 3840) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 441 time to evaluate : 1.186 Fit side-chains REVERT: A 149 LYS cc_start: 0.8079 (mmtt) cc_final: 0.7795 (mtmt) REVERT: A 208 MET cc_start: 0.8963 (mmm) cc_final: 0.8719 (mmm) REVERT: A 216 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6925 (tm-30) REVERT: A 429 GLN cc_start: 0.6828 (tp-100) cc_final: 0.6564 (tp-100) REVERT: B 208 MET cc_start: 0.8936 (mmm) cc_final: 0.8718 (mmm) REVERT: B 216 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6914 (tm-30) REVERT: B 429 GLN cc_start: 0.6971 (tp-100) cc_final: 0.6697 (tp-100) REVERT: C 23 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7186 (mt-10) REVERT: C 216 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6830 (tm-30) REVERT: C 429 GLN cc_start: 0.6872 (tp-100) cc_final: 0.6455 (tp-100) REVERT: D 23 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7183 (mt-10) REVERT: D 149 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7709 (mtmt) REVERT: D 216 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6866 (tm-30) REVERT: D 217 GLU cc_start: 0.7270 (mt-10) cc_final: 0.7054 (mt-10) REVERT: D 252 MET cc_start: 0.9283 (ptm) cc_final: 0.9025 (ptm) REVERT: D 429 GLN cc_start: 0.6873 (tp-100) cc_final: 0.6535 (tp-100) REVERT: E 65 GLN cc_start: 0.6959 (pt0) cc_final: 0.6626 (pt0) REVERT: E 149 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7789 (mtmt) REVERT: E 208 MET cc_start: 0.8917 (mmm) cc_final: 0.8678 (mmm) REVERT: E 216 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6891 (tm-30) REVERT: E 429 GLN cc_start: 0.6942 (tp-100) cc_final: 0.6679 (tp-100) REVERT: F 149 LYS cc_start: 0.8107 (mmtt) cc_final: 0.7791 (mtmt) REVERT: F 208 MET cc_start: 0.8952 (mmm) cc_final: 0.8727 (mmm) REVERT: F 216 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6851 (tm-30) REVERT: F 429 GLN cc_start: 0.6821 (tp-100) cc_final: 0.6548 (tp-100) REVERT: G 65 GLN cc_start: 0.7020 (pt0) cc_final: 0.6710 (pt0) REVERT: G 149 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7822 (mtmt) REVERT: G 208 MET cc_start: 0.8935 (mmm) cc_final: 0.8726 (mmm) REVERT: G 216 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6933 (tm-30) REVERT: G 429 GLN cc_start: 0.6902 (tp-100) cc_final: 0.6645 (tp-100) REVERT: H 208 MET cc_start: 0.8932 (mmm) cc_final: 0.8729 (mmm) REVERT: H 216 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6932 (tm-30) REVERT: H 429 GLN cc_start: 0.6883 (tp-100) cc_final: 0.6615 (tp-100) outliers start: 8 outliers final: 8 residues processed: 441 average time/residue: 1.1271 time to fit residues: 551.6209 Evaluate side-chains 411 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 403 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 311 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.0020 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.0570 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.0970 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.2980 overall best weight: 0.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN C 345 GLN D 109 ASN D 345 GLN E 345 GLN F 345 GLN G 345 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.142187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.128984 restraints weight = 26292.020| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 0.80 r_work: 0.3383 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 29096 Z= 0.104 Angle : 0.492 4.881 39472 Z= 0.259 Chirality : 0.039 0.134 4152 Planarity : 0.004 0.024 5168 Dihedral : 9.150 178.678 4144 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.77 % Allowed : 11.97 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.15), residues: 3544 helix: 1.78 (0.13), residues: 1632 sheet: 0.51 (0.23), residues: 504 loop : 1.16 (0.18), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 442 TYR 0.018 0.001 TYR D 263 PHE 0.010 0.001 PHE G 297 TRP 0.008 0.001 TRP H 63 HIS 0.004 0.001 HIS F 393 Details of bonding type rmsd covalent geometry : bond 0.00218 (29096) covalent geometry : angle 0.49151 (39472) hydrogen bonds : bond 0.03748 ( 1384) hydrogen bonds : angle 5.43658 ( 3840) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 431 time to evaluate : 1.100 Fit side-chains REVERT: A 149 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7951 (mtmt) REVERT: A 208 MET cc_start: 0.9130 (mmm) cc_final: 0.8813 (mmm) REVERT: A 276 MET cc_start: 0.9079 (mtm) cc_final: 0.8826 (mtm) REVERT: A 277 ILE cc_start: 0.8354 (mt) cc_final: 0.7856 (mt) REVERT: A 429 GLN cc_start: 0.7531 (tp-100) cc_final: 0.7310 (tp-100) REVERT: B 149 LYS cc_start: 0.8455 (mttt) cc_final: 0.8088 (mtmt) REVERT: B 208 MET cc_start: 0.9117 (mmm) cc_final: 0.8830 (mmm) REVERT: B 216 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7359 (tm-30) REVERT: B 429 GLN cc_start: 0.7639 (tp-100) cc_final: 0.7333 (tp-100) REVERT: C 208 MET cc_start: 0.9096 (mmm) cc_final: 0.8730 (mmp) REVERT: C 216 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7338 (tm-30) REVERT: C 429 GLN cc_start: 0.7568 (tp-100) cc_final: 0.7365 (tp-100) REVERT: D 149 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7894 (mtmt) REVERT: D 208 MET cc_start: 0.9094 (mmm) cc_final: 0.8766 (mmp) REVERT: D 216 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7439 (tm-30) REVERT: D 276 MET cc_start: 0.9043 (mtm) cc_final: 0.8821 (mtm) REVERT: E 149 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7924 (mtmt) REVERT: E 208 MET cc_start: 0.9131 (mmm) cc_final: 0.8812 (mmm) REVERT: E 216 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7321 (tm-30) REVERT: E 277 ILE cc_start: 0.8351 (mt) cc_final: 0.7800 (mt) REVERT: E 429 GLN cc_start: 0.7608 (tp-100) cc_final: 0.7315 (tp-100) REVERT: F 208 MET cc_start: 0.9142 (mmm) cc_final: 0.8848 (mmm) REVERT: F 216 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7350 (tm-30) REVERT: F 276 MET cc_start: 0.9093 (mtm) cc_final: 0.8856 (mtm) REVERT: F 277 ILE cc_start: 0.8378 (mt) cc_final: 0.7978 (mt) REVERT: F 429 GLN cc_start: 0.7556 (tp-100) cc_final: 0.7355 (tp-100) REVERT: G 208 MET cc_start: 0.9119 (mmm) cc_final: 0.8839 (mmm) REVERT: G 216 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7362 (tm-30) REVERT: G 234 GLU cc_start: 0.8065 (mp0) cc_final: 0.7849 (mp0) REVERT: G 276 MET cc_start: 0.9080 (mtm) cc_final: 0.8852 (mtm) REVERT: G 429 GLN cc_start: 0.7604 (tp-100) cc_final: 0.7297 (tp-100) REVERT: H 208 MET cc_start: 0.9110 (mmm) cc_final: 0.8834 (mmm) REVERT: H 216 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7362 (tm-30) REVERT: H 429 GLN cc_start: 0.7555 (tp-100) cc_final: 0.7300 (tp-100) outliers start: 50 outliers final: 10 residues processed: 447 average time/residue: 1.0779 time to fit residues: 537.8803 Evaluate side-chains 403 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 393 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 311 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 107 optimal weight: 0.7980 chunk 160 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 319 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN B 193 ASN B 345 GLN C 193 ASN C 345 GLN D 193 ASN D 345 GLN D 429 GLN E 193 ASN E 345 GLN F 193 ASN F 345 GLN G 193 ASN ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 429 GLN H 193 ASN H 345 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.130685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116852 restraints weight = 26196.032| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 0.81 r_work: 0.3224 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 29096 Z= 0.172 Angle : 0.578 6.625 39472 Z= 0.305 Chirality : 0.042 0.134 4152 Planarity : 0.004 0.027 5168 Dihedral : 9.182 171.417 4144 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.38 % Allowed : 12.29 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.14), residues: 3544 helix: 1.57 (0.13), residues: 1584 sheet: 0.74 (0.22), residues: 512 loop : 1.05 (0.18), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 34 TYR 0.028 0.002 TYR B 263 PHE 0.021 0.002 PHE F 297 TRP 0.013 0.002 TRP E 354 HIS 0.004 0.001 HIS H 280 Details of bonding type rmsd covalent geometry : bond 0.00373 (29096) covalent geometry : angle 0.57838 (39472) hydrogen bonds : bond 0.04682 ( 1384) hydrogen bonds : angle 5.43358 ( 3840) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 413 time to evaluate : 1.017 Fit side-chains REVERT: A 65 GLN cc_start: 0.7610 (pt0) cc_final: 0.7326 (pt0) REVERT: A 429 GLN cc_start: 0.7791 (tp40) cc_final: 0.7568 (tp-100) REVERT: B 65 GLN cc_start: 0.7599 (pt0) cc_final: 0.7321 (pt0) REVERT: B 216 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7361 (tm-30) REVERT: B 429 GLN cc_start: 0.7806 (tp-100) cc_final: 0.7605 (tp-100) REVERT: C 65 GLN cc_start: 0.7615 (pt0) cc_final: 0.7363 (pt0) REVERT: C 216 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7380 (tm-30) REVERT: C 429 GLN cc_start: 0.7773 (tp-100) cc_final: 0.7524 (tp-100) REVERT: D 216 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7430 (tm-30) REVERT: D 429 GLN cc_start: 0.7769 (tp40) cc_final: 0.7155 (tp-100) REVERT: E 65 GLN cc_start: 0.7594 (pt0) cc_final: 0.7310 (pt0) REVERT: E 216 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7449 (tm-30) REVERT: F 65 GLN cc_start: 0.7598 (pt0) cc_final: 0.7344 (pt0) REVERT: F 216 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7401 (tm-30) REVERT: G 216 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7480 (tm-30) REVERT: G 429 GLN cc_start: 0.7798 (tp40) cc_final: 0.7571 (tp-100) REVERT: H 216 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7391 (tm-30) outliers start: 39 outliers final: 18 residues processed: 432 average time/residue: 1.1464 time to fit residues: 548.5123 Evaluate side-chains 425 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 407 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 311 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 95 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 251 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 307 optimal weight: 4.9990 chunk 269 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 0.0970 chunk 26 optimal weight: 3.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 GLN B 429 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 GLN ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 GLN ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 GLN ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 429 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.126870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.112970 restraints weight = 25986.878| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 0.81 r_work: 0.3158 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 29096 Z= 0.250 Angle : 0.674 8.162 39472 Z= 0.355 Chirality : 0.046 0.148 4152 Planarity : 0.005 0.035 5168 Dihedral : 9.711 171.110 4144 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.94 % Allowed : 12.71 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.14), residues: 3544 helix: 1.16 (0.12), residues: 1576 sheet: 0.42 (0.22), residues: 488 loop : 0.80 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 442 TYR 0.033 0.003 TYR G 263 PHE 0.024 0.003 PHE C 297 TRP 0.018 0.002 TRP C 354 HIS 0.005 0.002 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00546 (29096) covalent geometry : angle 0.67418 (39472) hydrogen bonds : bond 0.05392 ( 1384) hydrogen bonds : angle 5.72744 ( 3840) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 421 time to evaluate : 0.834 Fit side-chains REVERT: A 173 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8122 (ttt-90) REVERT: A 216 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: A 252 MET cc_start: 0.9445 (OUTLIER) cc_final: 0.8762 (ptm) REVERT: B 173 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7998 (ttt-90) REVERT: B 216 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7335 (tm-30) REVERT: B 429 GLN cc_start: 0.8080 (tp40) cc_final: 0.7831 (tp-100) REVERT: C 65 GLN cc_start: 0.7684 (pt0) cc_final: 0.7463 (pt0) REVERT: C 173 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8078 (ttt-90) REVERT: C 216 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7361 (tm-30) REVERT: C 252 MET cc_start: 0.9440 (OUTLIER) cc_final: 0.8767 (ptm) REVERT: D 65 GLN cc_start: 0.7591 (pt0) cc_final: 0.7334 (pt0) REVERT: D 173 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8075 (ttt-90) REVERT: D 216 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7403 (tm-30) REVERT: D 252 MET cc_start: 0.9437 (OUTLIER) cc_final: 0.8758 (ptm) REVERT: D 429 GLN cc_start: 0.8062 (tp40) cc_final: 0.7639 (mm-40) REVERT: E 65 GLN cc_start: 0.7680 (pt0) cc_final: 0.7475 (pt0) REVERT: E 173 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7987 (ttt-90) REVERT: E 216 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7356 (tm-30) REVERT: E 234 GLU cc_start: 0.8187 (mp0) cc_final: 0.7981 (mp0) REVERT: E 252 MET cc_start: 0.9440 (OUTLIER) cc_final: 0.8756 (ptm) REVERT: E 429 GLN cc_start: 0.7985 (tp40) cc_final: 0.7537 (tp-100) REVERT: F 65 GLN cc_start: 0.7678 (pt0) cc_final: 0.7370 (pt0) REVERT: F 216 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7372 (tm-30) REVERT: F 429 GLN cc_start: 0.8005 (tp40) cc_final: 0.7534 (tp-100) REVERT: G 173 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8120 (ttt-90) REVERT: G 216 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7378 (tm-30) REVERT: H 65 GLN cc_start: 0.7588 (pt0) cc_final: 0.7347 (pt0) REVERT: H 173 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8129 (ttt-90) REVERT: H 216 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7352 (tm-30) REVERT: H 252 MET cc_start: 0.9434 (OUTLIER) cc_final: 0.8758 (ptm) REVERT: H 429 GLN cc_start: 0.7989 (tp40) cc_final: 0.7552 (tp-100) outliers start: 55 outliers final: 31 residues processed: 459 average time/residue: 1.0438 time to fit residues: 530.0974 Evaluate side-chains 452 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 408 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 252 MET Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 311 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 294 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 178 optimal weight: 0.5980 chunk 286 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.128517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.114915 restraints weight = 26181.030| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 0.80 r_work: 0.3196 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 29096 Z= 0.178 Angle : 0.596 6.869 39472 Z= 0.315 Chirality : 0.042 0.135 4152 Planarity : 0.004 0.028 5168 Dihedral : 9.574 171.218 4144 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.30 % Allowed : 12.71 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.14), residues: 3544 helix: 1.20 (0.12), residues: 1576 sheet: 0.38 (0.22), residues: 488 loop : 0.81 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 442 TYR 0.028 0.002 TYR B 263 PHE 0.019 0.002 PHE G 297 TRP 0.016 0.002 TRP E 354 HIS 0.004 0.001 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00386 (29096) covalent geometry : angle 0.59632 (39472) hydrogen bonds : bond 0.04733 ( 1384) hydrogen bonds : angle 5.57130 ( 3840) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 421 time to evaluate : 1.077 Fit side-chains REVERT: A 173 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8019 (ttt-90) REVERT: A 216 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: A 252 MET cc_start: 0.9422 (OUTLIER) cc_final: 0.8743 (ptm) REVERT: A 429 GLN cc_start: 0.8034 (tp-100) cc_final: 0.7701 (tp-100) REVERT: B 117 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8010 (ttp-170) REVERT: B 173 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8017 (ttt-90) REVERT: B 216 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7322 (tm-30) REVERT: B 429 GLN cc_start: 0.8001 (tp40) cc_final: 0.7775 (tp-100) REVERT: C 65 GLN cc_start: 0.7664 (pt0) cc_final: 0.7418 (pt0) REVERT: C 173 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8017 (ttt-90) REVERT: C 216 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7310 (tm-30) REVERT: C 252 MET cc_start: 0.9417 (OUTLIER) cc_final: 0.8755 (ptm) REVERT: C 429 GLN cc_start: 0.8100 (tp-100) cc_final: 0.7753 (tp-100) REVERT: D 65 GLN cc_start: 0.7545 (pt0) cc_final: 0.7280 (pt0) REVERT: D 173 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8026 (ttt-90) REVERT: D 216 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7369 (tm-30) REVERT: D 252 MET cc_start: 0.9420 (OUTLIER) cc_final: 0.8743 (ptm) REVERT: D 429 GLN cc_start: 0.8053 (tp40) cc_final: 0.7638 (tp-100) REVERT: E 173 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8024 (ttt-90) REVERT: E 216 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7334 (tm-30) REVERT: E 252 MET cc_start: 0.9417 (OUTLIER) cc_final: 0.8734 (ptm) REVERT: E 429 GLN cc_start: 0.8012 (tp40) cc_final: 0.7500 (tp-100) REVERT: F 65 GLN cc_start: 0.7651 (pt0) cc_final: 0.7409 (pt0) REVERT: F 216 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7327 (tm-30) REVERT: F 429 GLN cc_start: 0.8038 (tp40) cc_final: 0.7475 (tp-100) REVERT: G 173 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7981 (ttt-90) REVERT: G 216 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7323 (tm-30) REVERT: G 429 GLN cc_start: 0.8029 (tp-100) cc_final: 0.7695 (tp-100) REVERT: H 65 GLN cc_start: 0.7535 (pt0) cc_final: 0.7300 (pt0) REVERT: H 173 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8029 (ttt-90) REVERT: H 216 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7342 (tm-30) REVERT: H 252 MET cc_start: 0.9425 (OUTLIER) cc_final: 0.8743 (ptm) outliers start: 65 outliers final: 31 residues processed: 465 average time/residue: 1.1093 time to fit residues: 570.8798 Evaluate side-chains 461 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 416 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 252 MET Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 311 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 259 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 282 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 168 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 235 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 310 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 GLN ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.128349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.114716 restraints weight = 26093.889| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 0.80 r_work: 0.3185 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 29096 Z= 0.181 Angle : 0.604 6.999 39472 Z= 0.319 Chirality : 0.042 0.136 4152 Planarity : 0.004 0.028 5168 Dihedral : 9.603 170.358 4144 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.91 % Allowed : 13.38 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.14), residues: 3544 helix: 1.18 (0.12), residues: 1576 sheet: 0.32 (0.22), residues: 488 loop : 0.84 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 442 TYR 0.029 0.002 TYR F 263 PHE 0.020 0.002 PHE F 297 TRP 0.017 0.002 TRP H 354 HIS 0.004 0.001 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00394 (29096) covalent geometry : angle 0.60386 (39472) hydrogen bonds : bond 0.04777 ( 1384) hydrogen bonds : angle 5.56399 ( 3840) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 420 time to evaluate : 1.136 Fit side-chains REVERT: A 173 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8064 (ttt-90) REVERT: A 216 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: A 252 MET cc_start: 0.9429 (OUTLIER) cc_final: 0.8744 (ptm) REVERT: B 173 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8019 (ttt-90) REVERT: B 216 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7307 (tm-30) REVERT: B 252 MET cc_start: 0.9431 (OUTLIER) cc_final: 0.8721 (ptm) REVERT: B 429 GLN cc_start: 0.7993 (tp40) cc_final: 0.7728 (tp-100) REVERT: C 173 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8019 (ttt-90) REVERT: C 216 GLU cc_start: 0.7494 (tm-30) cc_final: 0.7188 (tm-30) REVERT: C 252 MET cc_start: 0.9423 (OUTLIER) cc_final: 0.8756 (ptm) REVERT: C 429 GLN cc_start: 0.8096 (tp-100) cc_final: 0.7723 (tp-100) REVERT: D 65 GLN cc_start: 0.7576 (pt0) cc_final: 0.7368 (pt0) REVERT: D 173 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8028 (ttt-90) REVERT: D 216 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7351 (tm-30) REVERT: D 252 MET cc_start: 0.9426 (OUTLIER) cc_final: 0.8741 (ptm) REVERT: D 429 GLN cc_start: 0.8070 (tp40) cc_final: 0.7671 (tp-100) REVERT: E 65 GLN cc_start: 0.7576 (pt0) cc_final: 0.7369 (pt0) REVERT: E 173 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8015 (ttt-90) REVERT: E 216 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7314 (tm-30) REVERT: E 234 GLU cc_start: 0.8206 (mp0) cc_final: 0.7994 (mp0) REVERT: E 252 MET cc_start: 0.9421 (OUTLIER) cc_final: 0.8736 (ptm) REVERT: E 429 GLN cc_start: 0.8009 (tp40) cc_final: 0.7641 (tp-100) REVERT: F 216 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7297 (tm-30) REVERT: F 252 MET cc_start: 0.9426 (OUTLIER) cc_final: 0.8718 (ptm) REVERT: F 429 GLN cc_start: 0.8036 (tp40) cc_final: 0.7620 (tp-100) REVERT: G 173 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8000 (ttt-90) REVERT: G 216 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7301 (tm-30) REVERT: G 252 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.8723 (ptm) REVERT: H 65 GLN cc_start: 0.7571 (pt0) cc_final: 0.7298 (pt0) REVERT: H 173 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8083 (ttt-90) REVERT: H 216 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7327 (tm-30) REVERT: H 252 MET cc_start: 0.9426 (OUTLIER) cc_final: 0.8739 (ptm) REVERT: H 429 GLN cc_start: 0.8023 (tp40) cc_final: 0.7605 (tp-100) outliers start: 54 outliers final: 35 residues processed: 456 average time/residue: 1.0769 time to fit residues: 544.3449 Evaluate side-chains 467 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 416 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 252 MET Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 252 MET Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 252 MET Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 311 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 41 optimal weight: 2.9990 chunk 290 optimal weight: 10.0000 chunk 230 optimal weight: 0.5980 chunk 231 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 315 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.129947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116199 restraints weight = 26080.760| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 0.81 r_work: 0.3220 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 29096 Z= 0.152 Angle : 0.573 6.394 39472 Z= 0.302 Chirality : 0.041 0.131 4152 Planarity : 0.004 0.029 5168 Dihedral : 9.450 170.101 4144 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.30 % Allowed : 14.05 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.14), residues: 3544 helix: 1.13 (0.12), residues: 1624 sheet: 0.49 (0.23), residues: 472 loop : 0.97 (0.18), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 442 TYR 0.027 0.002 TYR A 263 PHE 0.017 0.002 PHE F 297 TRP 0.016 0.001 TRP F 354 HIS 0.004 0.001 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00330 (29096) covalent geometry : angle 0.57343 (39472) hydrogen bonds : bond 0.04447 ( 1384) hydrogen bonds : angle 5.46613 ( 3840) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 418 time to evaluate : 0.962 Fit side-chains REVERT: A 173 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7980 (ttt-90) REVERT: A 216 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7523 (tm-30) REVERT: A 252 MET cc_start: 0.9414 (OUTLIER) cc_final: 0.8742 (ptm) REVERT: A 429 GLN cc_start: 0.8032 (tp-100) cc_final: 0.7664 (tp-100) REVERT: B 117 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7983 (ttp-170) REVERT: B 173 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8008 (ttt-90) REVERT: B 216 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7167 (tm-30) REVERT: B 252 MET cc_start: 0.9416 (OUTLIER) cc_final: 0.8724 (ptm) REVERT: B 429 GLN cc_start: 0.7991 (tp40) cc_final: 0.7716 (tp-100) REVERT: C 65 GLN cc_start: 0.7549 (pt0) cc_final: 0.7326 (pt0) REVERT: C 173 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8001 (ttt-90) REVERT: C 216 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7167 (tm-30) REVERT: C 252 MET cc_start: 0.9403 (OUTLIER) cc_final: 0.8755 (ptm) REVERT: C 429 GLN cc_start: 0.8074 (tp-100) cc_final: 0.7700 (tp-100) REVERT: D 65 GLN cc_start: 0.7555 (pt0) cc_final: 0.7326 (pt0) REVERT: D 173 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8024 (ttt-90) REVERT: D 216 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7297 (tm-30) REVERT: D 252 MET cc_start: 0.9411 (OUTLIER) cc_final: 0.8739 (ptm) REVERT: D 429 GLN cc_start: 0.8063 (tp40) cc_final: 0.7644 (tp-100) REVERT: E 65 GLN cc_start: 0.7579 (pt0) cc_final: 0.7323 (pt0) REVERT: E 173 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7983 (ttt-90) REVERT: E 216 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7278 (tm-30) REVERT: E 252 MET cc_start: 0.9408 (OUTLIER) cc_final: 0.8735 (ptm) REVERT: E 429 GLN cc_start: 0.7984 (tp40) cc_final: 0.7605 (tp-100) REVERT: F 65 GLN cc_start: 0.7546 (pt0) cc_final: 0.7326 (pt0) REVERT: F 216 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7173 (tm-30) REVERT: F 252 MET cc_start: 0.9412 (OUTLIER) cc_final: 0.8724 (ptm) REVERT: F 429 GLN cc_start: 0.8036 (tp40) cc_final: 0.7616 (tp-100) REVERT: G 173 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7983 (ttt-90) REVERT: G 216 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7122 (tm-30) REVERT: G 252 MET cc_start: 0.9416 (OUTLIER) cc_final: 0.8726 (ptm) REVERT: G 429 GLN cc_start: 0.8037 (tp-100) cc_final: 0.7667 (tp-100) REVERT: H 65 GLN cc_start: 0.7555 (pt0) cc_final: 0.7343 (pt0) REVERT: H 173 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7997 (ttt-90) REVERT: H 216 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7180 (tm-30) REVERT: H 252 MET cc_start: 0.9412 (OUTLIER) cc_final: 0.8741 (ptm) REVERT: H 338 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7097 (mm-30) REVERT: H 429 GLN cc_start: 0.8052 (tp40) cc_final: 0.7649 (tp-100) outliers start: 65 outliers final: 48 residues processed: 465 average time/residue: 1.0182 time to fit residues: 526.7894 Evaluate side-chains 480 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 415 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 252 MET Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 252 MET Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 378 SER Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 252 MET Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 311 HIS Chi-restraints excluded: chain H residue 378 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 16 optimal weight: 4.9990 chunk 81 optimal weight: 0.2980 chunk 140 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 232 optimal weight: 0.6980 chunk 329 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.127806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.114210 restraints weight = 26117.616| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 0.80 r_work: 0.3187 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 29096 Z= 0.197 Angle : 0.625 7.165 39472 Z= 0.329 Chirality : 0.043 0.141 4152 Planarity : 0.004 0.029 5168 Dihedral : 9.640 170.089 4144 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.37 % Allowed : 14.23 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.14), residues: 3544 helix: 1.02 (0.12), residues: 1624 sheet: 0.42 (0.23), residues: 472 loop : 0.94 (0.18), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 442 TYR 0.031 0.002 TYR A 263 PHE 0.021 0.003 PHE F 297 TRP 0.018 0.002 TRP G 354 HIS 0.004 0.001 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00432 (29096) covalent geometry : angle 0.62475 (39472) hydrogen bonds : bond 0.04917 ( 1384) hydrogen bonds : angle 5.59060 ( 3840) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 422 time to evaluate : 1.245 Fit side-chains REVERT: A 173 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8065 (ttt-90) REVERT: A 216 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7520 (tm-30) REVERT: B 173 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8094 (ttt-90) REVERT: B 216 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7291 (tm-30) REVERT: B 252 MET cc_start: 0.9444 (OUTLIER) cc_final: 0.8715 (ptm) REVERT: C 65 GLN cc_start: 0.7565 (pt0) cc_final: 0.7321 (pt0) REVERT: C 173 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8009 (ttt-90) REVERT: C 216 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7239 (tm-30) REVERT: D 173 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8025 (ttt-90) REVERT: D 216 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7308 (tm-30) REVERT: D 252 MET cc_start: 0.9436 (OUTLIER) cc_final: 0.8741 (ptm) REVERT: D 429 GLN cc_start: 0.8097 (tp40) cc_final: 0.7690 (tp-100) REVERT: E 173 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8070 (ttt-90) REVERT: E 216 GLU cc_start: 0.7492 (tm-30) cc_final: 0.7286 (tm-30) REVERT: E 429 GLN cc_start: 0.8046 (tp40) cc_final: 0.7703 (tp-100) REVERT: F 65 GLN cc_start: 0.7555 (pt0) cc_final: 0.7315 (pt0) REVERT: F 216 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7276 (tm-30) REVERT: F 252 MET cc_start: 0.9437 (OUTLIER) cc_final: 0.8723 (ptm) REVERT: F 429 GLN cc_start: 0.8052 (tp40) cc_final: 0.7659 (tp-100) REVERT: G 173 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8057 (ttt-90) REVERT: G 216 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7279 (tm-30) REVERT: G 252 MET cc_start: 0.9440 (OUTLIER) cc_final: 0.8726 (ptm) REVERT: H 65 GLN cc_start: 0.7627 (pt0) cc_final: 0.7387 (pt0) REVERT: H 173 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8092 (ttt-90) REVERT: H 216 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7304 (tm-30) REVERT: H 429 GLN cc_start: 0.8049 (tp40) cc_final: 0.7671 (tp-100) outliers start: 67 outliers final: 48 residues processed: 476 average time/residue: 1.1498 time to fit residues: 607.5032 Evaluate side-chains 482 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 422 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 252 MET Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 252 MET Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 378 SER Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 311 HIS Chi-restraints excluded: chain H residue 378 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 194 optimal weight: 4.9990 chunk 351 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 175 optimal weight: 0.5980 chunk 187 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 322 optimal weight: 0.0570 chunk 346 optimal weight: 5.9990 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.131756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.118119 restraints weight = 26034.521| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 0.81 r_work: 0.3246 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 29096 Z= 0.130 Angle : 0.552 5.892 39472 Z= 0.292 Chirality : 0.040 0.131 4152 Planarity : 0.004 0.032 5168 Dihedral : 9.322 169.708 4144 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.01 % Allowed : 15.08 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.14), residues: 3544 helix: 1.04 (0.13), residues: 1672 sheet: 0.69 (0.25), residues: 400 loop : 0.61 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 442 TYR 0.025 0.002 TYR B 263 PHE 0.015 0.002 PHE F 297 TRP 0.016 0.001 TRP A 354 HIS 0.004 0.001 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00280 (29096) covalent geometry : angle 0.55248 (39472) hydrogen bonds : bond 0.04149 ( 1384) hydrogen bonds : angle 5.36686 ( 3840) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 420 time to evaluate : 1.173 Fit side-chains REVERT: A 173 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7967 (ttt-90) REVERT: A 216 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7417 (tm-30) REVERT: A 252 MET cc_start: 0.9410 (OUTLIER) cc_final: 0.8713 (ptm) REVERT: A 429 GLN cc_start: 0.7955 (tp-100) cc_final: 0.7589 (tp-100) REVERT: B 117 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7994 (ttp-170) REVERT: B 173 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7952 (ttt-90) REVERT: B 216 GLU cc_start: 0.7404 (tm-30) cc_final: 0.7081 (tm-30) REVERT: B 252 MET cc_start: 0.9413 (OUTLIER) cc_final: 0.8718 (ptm) REVERT: B 429 GLN cc_start: 0.7992 (tp-100) cc_final: 0.7679 (tp-100) REVERT: C 173 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7948 (ttt-90) REVERT: C 216 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7078 (tm-30) REVERT: C 252 MET cc_start: 0.9400 (OUTLIER) cc_final: 0.8735 (ptm) REVERT: C 429 GLN cc_start: 0.7991 (tp-100) cc_final: 0.7613 (tp-100) REVERT: D 173 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7875 (ttt-90) REVERT: D 216 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7113 (tm-30) REVERT: D 252 MET cc_start: 0.9399 (OUTLIER) cc_final: 0.8736 (ptm) REVERT: D 429 GLN cc_start: 0.8033 (tp40) cc_final: 0.7553 (tp-100) REVERT: E 173 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7963 (ttt-90) REVERT: E 216 GLU cc_start: 0.7406 (tm-30) cc_final: 0.7154 (tm-30) REVERT: E 252 MET cc_start: 0.9407 (OUTLIER) cc_final: 0.8712 (ptm) REVERT: E 429 GLN cc_start: 0.7995 (tp40) cc_final: 0.7591 (tp40) REVERT: F 216 GLU cc_start: 0.7407 (tm-30) cc_final: 0.7077 (tm-30) REVERT: F 252 MET cc_start: 0.9409 (OUTLIER) cc_final: 0.8717 (ptm) REVERT: F 429 GLN cc_start: 0.7986 (tp40) cc_final: 0.7486 (tp40) REVERT: G 173 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7956 (ttt-90) REVERT: G 216 GLU cc_start: 0.7404 (tm-30) cc_final: 0.7153 (tm-30) REVERT: G 252 MET cc_start: 0.9416 (OUTLIER) cc_final: 0.8725 (ptm) REVERT: G 429 GLN cc_start: 0.7966 (tp-100) cc_final: 0.7598 (tp-100) REVERT: H 65 GLN cc_start: 0.7538 (pt0) cc_final: 0.7312 (pt0) REVERT: H 173 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7986 (ttt-90) REVERT: H 216 GLU cc_start: 0.7414 (tm-30) cc_final: 0.7095 (tm-30) REVERT: H 252 MET cc_start: 0.9426 (OUTLIER) cc_final: 0.9006 (ptm) REVERT: H 338 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7128 (mm-30) REVERT: H 429 GLN cc_start: 0.7990 (tp40) cc_final: 0.7522 (tp40) outliers start: 57 outliers final: 34 residues processed: 466 average time/residue: 1.0711 time to fit residues: 554.1718 Evaluate side-chains 467 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 416 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 252 MET Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 252 MET Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 378 SER Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 252 MET Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 311 HIS Chi-restraints excluded: chain H residue 378 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 47 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 349 optimal weight: 0.9980 chunk 223 optimal weight: 5.9990 chunk 268 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 289 optimal weight: 0.8980 chunk 261 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.130026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.116491 restraints weight = 26068.008| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 0.80 r_work: 0.3231 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 29096 Z= 0.147 Angle : 0.577 6.151 39472 Z= 0.304 Chirality : 0.041 0.131 4152 Planarity : 0.004 0.040 5168 Dihedral : 9.347 169.460 4144 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.08 % Allowed : 15.57 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.14), residues: 3544 helix: 1.02 (0.12), residues: 1672 sheet: 0.44 (0.23), residues: 472 loop : 0.70 (0.18), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 442 TYR 0.027 0.002 TYR B 263 PHE 0.017 0.002 PHE F 297 TRP 0.016 0.001 TRP C 354 HIS 0.004 0.001 HIS G 311 Details of bonding type rmsd covalent geometry : bond 0.00319 (29096) covalent geometry : angle 0.57672 (39472) hydrogen bonds : bond 0.04356 ( 1384) hydrogen bonds : angle 5.39490 ( 3840) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 416 time to evaluate : 1.055 Fit side-chains REVERT: A 173 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7974 (ttt-90) REVERT: A 216 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7460 (tm-30) REVERT: A 252 MET cc_start: 0.9423 (OUTLIER) cc_final: 0.8720 (ptm) REVERT: A 429 GLN cc_start: 0.7964 (tp-100) cc_final: 0.7597 (tp-100) REVERT: B 173 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7895 (ttt-90) REVERT: B 216 GLU cc_start: 0.7408 (tm-30) cc_final: 0.7151 (tm-30) REVERT: B 252 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.8739 (ptm) REVERT: C 173 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7895 (ttt-90) REVERT: C 216 GLU cc_start: 0.7414 (tm-30) cc_final: 0.7160 (tm-30) REVERT: C 252 MET cc_start: 0.9405 (OUTLIER) cc_final: 0.8725 (ptm) REVERT: C 429 GLN cc_start: 0.7968 (tp-100) cc_final: 0.7586 (tp-100) REVERT: D 173 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7930 (ttt-90) REVERT: D 216 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7193 (tm-30) REVERT: D 252 MET cc_start: 0.9409 (OUTLIER) cc_final: 0.8741 (ptm) REVERT: D 429 GLN cc_start: 0.8020 (tp40) cc_final: 0.7598 (tp-100) REVERT: E 173 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7976 (ttt-90) REVERT: E 216 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7160 (tm-30) REVERT: E 252 MET cc_start: 0.9418 (OUTLIER) cc_final: 0.8715 (ptm) REVERT: E 429 GLN cc_start: 0.8049 (tp40) cc_final: 0.7651 (tp-100) REVERT: F 216 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7157 (tm-30) REVERT: F 252 MET cc_start: 0.9424 (OUTLIER) cc_final: 0.8736 (ptm) REVERT: F 429 GLN cc_start: 0.8024 (tp40) cc_final: 0.7589 (tp-100) REVERT: G 173 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7972 (ttt-90) REVERT: G 216 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7158 (tm-30) REVERT: G 252 MET cc_start: 0.9431 (OUTLIER) cc_final: 0.8742 (ptm) REVERT: G 429 GLN cc_start: 0.7972 (tp-100) cc_final: 0.7601 (tp-100) REVERT: H 65 GLN cc_start: 0.7544 (pt0) cc_final: 0.7298 (pt0) REVERT: H 173 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7992 (ttt-90) REVERT: H 216 GLU cc_start: 0.7426 (tm-30) cc_final: 0.7172 (tm-30) REVERT: H 252 MET cc_start: 0.9431 (OUTLIER) cc_final: 0.8734 (ptm) REVERT: H 429 GLN cc_start: 0.8026 (tp40) cc_final: 0.7620 (tp-100) outliers start: 59 outliers final: 40 residues processed: 464 average time/residue: 1.1402 time to fit residues: 586.4572 Evaluate side-chains 474 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 418 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 252 MET Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain G residue 14 ARG Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 252 MET Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 378 SER Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 252 MET Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 311 HIS Chi-restraints excluded: chain H residue 378 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 260 optimal weight: 0.7980 chunk 224 optimal weight: 10.0000 chunk 338 optimal weight: 6.9990 chunk 345 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 214 optimal weight: 8.9990 chunk 300 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 231 optimal weight: 3.9990 chunk 304 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.130900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.117180 restraints weight = 26110.333| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 0.81 r_work: 0.3231 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 29096 Z= 0.147 Angle : 0.578 6.531 39472 Z= 0.304 Chirality : 0.041 0.130 4152 Planarity : 0.004 0.063 5168 Dihedral : 9.345 169.413 4144 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.26 % Allowed : 15.36 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.14), residues: 3544 helix: 1.02 (0.13), residues: 1672 sheet: 0.44 (0.23), residues: 472 loop : 0.69 (0.18), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 442 TYR 0.027 0.002 TYR A 263 PHE 0.017 0.002 PHE F 297 TRP 0.015 0.001 TRP F 354 HIS 0.004 0.001 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00319 (29096) covalent geometry : angle 0.57824 (39472) hydrogen bonds : bond 0.04334 ( 1384) hydrogen bonds : angle 5.38457 ( 3840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11411.10 seconds wall clock time: 195 minutes 37.90 seconds (11737.90 seconds total)